Summary information

PDB id
7xdh
Class
DNA
Method
X-ray (1.83 Å)
Summary
Crystal structure of a dimeric interlocked parallel g-quadruplex
Reference
Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT (2022): "Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A.G.G.G.G pentad in an interlocked G-quadruplex." Biochem.Biophys.Res.Commun., 613, 153-158. doi: 10.1016/j.bbrc.2022.04.020.
Abstract
93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K+ solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A•G•G•G•G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.
G4 notes
12 G-tetrads, 2 G4 helices, 4 G4 stems, 2 G4 coaxial stacks, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'-SEPARATED

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 12 G-tetrads

 1 glyco-bond=s--- sugar=---. groove=w--n planarity=0.093 type=planar nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13
 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.127 type=planar nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13
 3 glyco-bond=---- sugar=.-.- groove=---- planarity=0.086 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.238 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
 5 glyco-bond=---- sugar=.-.- groove=---- planarity=0.082 type=planar nts=4 GGGG B.DG3,B.DG7,B.DG10,B.DG14
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.208 type=other  nts=4 GGGG B.DG4,B.DG8,B.DG11,B.DG15
 7 glyco-bond=s--- sugar=-.-. groove=w--n planarity=0.117 type=planar nts=4 GGGG C.DG1,D.DG6,D.DG2,D.DG13
 8 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.120 type=planar nts=4 GGGG C.DG2,C.DG6,D.DG1,C.DG13
 9 glyco-bond=---- sugar=.-.- groove=---- planarity=0.103 type=planar nts=4 GGGG C.DG3,C.DG7,C.DG10,C.DG14
10 glyco-bond=---- sugar=---- groove=---- planarity=0.231 type=other  nts=4 GGGG C.DG4,C.DG8,C.DG11,C.DG15
11 glyco-bond=---- sugar=.-.- groove=---- planarity=0.085 type=planar nts=4 GGGG D.DG3,D.DG7,D.DG10,D.DG14
12 glyco-bond=---- sugar=---- groove=---- planarity=0.223 type=other  nts=4 GGGG D.DG4,D.DG8,D.DG11,D.DG15

List of 2 G4-helices

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
 2  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13
 4  glyco-bond=s--- sugar=---. groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13
 5  glyco-bond=---- sugar=.-.- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG7,B.DG3,B.DG14
 6  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,B.DG4,B.DG15
  step#1  mp(<<,backward) area=10.52 rise=3.42 twist=30.1
  step#2  mp(<<,backward) area=9.59  rise=3.34 twist=32.0
  step#3  mm(<>,outward)  area=11.70 rise=3.45 twist=21.4
  step#4  pm(>>,forward)  area=9.73  rise=3.36 twist=32.4
  step#5  pm(>>,forward)  area=11.17 rise=3.44 twist=29.6
  strand#1 DNA glyco-bond=---s-- sugar=-.--.- nts=6 GGGGGG A.DG4,A.DG3,A.DG2,A.DG1,B.DG10,B.DG11
  strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG8,A.DG7,A.DG6,B.DG6,B.DG7,B.DG8
  strand#3 DNA glyco-bond=--s--- sugar=-.--.- nts=6 GGGGGG A.DG11,A.DG10,B.DG1,B.DG2,B.DG3,B.DG4
  strand#4 DNA glyco-bond=------ sugar=---.-- nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15

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5 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
 2  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
  step#1  mp(<<,backward) area=10.52 rise=3.42 twist=30.1

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 2  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13
  step#2  mp(<<,backward) area=9.59  rise=3.34 twist=32.0

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 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13
 4  glyco-bond=s--- sugar=---. groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13
  step#3  mm(<>,outward)  area=11.70 rise=3.45 twist=21.4

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 4  glyco-bond=s--- sugar=---. groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13
 5  glyco-bond=---- sugar=.-.- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG7,B.DG3,B.DG14
  step#4  pm(>>,forward)  area=9.73  rise=3.36 twist=32.4

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 5  glyco-bond=---- sugar=.-.- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG7,B.DG3,B.DG14
 6  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,B.DG4,B.DG15
  step#5  pm(>>,forward)  area=11.17 rise=3.44 twist=29.6

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Helix#2, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG8,C.DG11,C.DG15
 2  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG10,C.DG14
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG C.DG2,C.DG6,D.DG1,C.DG13
 4  glyco-bond=s--- sugar=-.-. groove=w--n Major-->WC nts=4 GGGG C.DG1,D.DG6,D.DG2,D.DG13
 5  glyco-bond=---- sugar=.-.- groove=---- Major-->WC nts=4 GGGG D.DG10,D.DG7,D.DG3,D.DG14
 6  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG11,D.DG8,D.DG4,D.DG15
  step#1  mp(<<,backward) area=10.46 rise=3.44 twist=30.4
  step#2  mp(<<,backward) area=9.58  rise=3.33 twist=32.2
  step#3  mm(<>,outward)  area=11.97 rise=3.44 twist=20.7
  step#4  pm(>>,forward)  area=8.67  rise=3.40 twist=32.7
  step#5  pm(>>,forward)  area=10.53 rise=3.43 twist=29.9
  strand#1 DNA glyco-bond=---s-- sugar=-.--.- nts=6 GGGGGG C.DG4,C.DG3,C.DG2,C.DG1,D.DG10,D.DG11
  strand#2 DNA glyco-bond=------ sugar=---.-- nts=6 GGGGGG C.DG8,C.DG7,C.DG6,D.DG6,D.DG7,D.DG8
  strand#3 DNA glyco-bond=--s--- sugar=-.--.- nts=6 GGGGGG C.DG11,C.DG10,D.DG1,D.DG2,D.DG3,D.DG4
  strand#4 DNA glyco-bond=------ sugar=---.-- nts=6 GGGGGG C.DG15,C.DG14,C.DG13,D.DG13,D.DG14,D.DG15

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5 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG8,C.DG11,C.DG15
 2  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG10,C.DG14
  step#1  mp(<<,backward) area=10.46 rise=3.44 twist=30.4

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 2  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG10,C.DG14
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG C.DG2,C.DG6,D.DG1,C.DG13
  step#2  mp(<<,backward) area=9.58  rise=3.33 twist=32.2

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 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG C.DG2,C.DG6,D.DG1,C.DG13
 4  glyco-bond=s--- sugar=-.-. groove=w--n Major-->WC nts=4 GGGG C.DG1,D.DG6,D.DG2,D.DG13
  step#3  mm(<>,outward)  area=11.97 rise=3.44 twist=20.7

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 4  glyco-bond=s--- sugar=-.-. groove=w--n Major-->WC nts=4 GGGG C.DG1,D.DG6,D.DG2,D.DG13
 5  glyco-bond=---- sugar=.-.- groove=---- Major-->WC nts=4 GGGG D.DG10,D.DG7,D.DG3,D.DG14
  step#4  pm(>>,forward)  area=8.67  rise=3.40 twist=32.7

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 5  glyco-bond=---- sugar=.-.- groove=---- Major-->WC nts=4 GGGG D.DG10,D.DG7,D.DG3,D.DG14
 6  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG D.DG11,D.DG8,D.DG4,D.DG15
  step#5  pm(>>,forward)  area=10.53 rise=3.43 twist=29.9

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List of 4 G4-stems

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=10.52 rise=3.42 twist=30.1
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG10,A.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG A.DT5,A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 AG A.DA12,A.DG13

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG10,B.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG11,B.DG15
  step#1  pm(>>,forward)  area=11.17 rise=3.44 twist=29.6
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG B.DG3,B.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG7,B.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG B.DG10,B.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG B.DT5,B.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A B.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 AG B.DA12,B.DG13

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Stem#3, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG10,C.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG8,C.DG11,C.DG15
  step#1  pm(>>,forward)  area=10.46 rise=3.44 twist=30.4
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG C.DG3,C.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG C.DG7,C.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG C.DG10,C.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG C.DG14,C.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG C.DT5,C.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A C.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 AG C.DA12,C.DG13

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Stem#4, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=.-.- groove=---- WC-->Major nts=4 GGGG D.DG3,D.DG7,D.DG10,D.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG D.DG4,D.DG8,D.DG11,D.DG15
  step#1  pm(>>,forward)  area=10.53 rise=3.43 twist=29.9
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG D.DG3,D.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG7,D.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG D.DG10,D.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG14,D.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG D.DT5,D.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A D.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 AG D.DA12,D.DG13

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List of 2 G4 coaxial stacks

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5'-SEPARATED]
 2 G4 helix#2 contains 2 G4 stems: [#3,#4]  [5'/5'-SEPARATED]